human cytomegalovirus manipulation of latently infected cells
TRANSCRIPT
Viruses 2013, 5, 2803-2824; doi:10.3390/v5112803
viruses ISSN 1999-4915
www.mdpi.com/journal/viruses
Review
Human Cytomegalovirus Manipulation of Latently Infected Cells
John H. Sinclair 1 and Matthew B. Reeves
2,*
1 Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Hills Road,
Cambridge, CB2 0QQ, UK; E-Mail: [email protected]
2 Institute of Immunity and Transplantation, Division of Infection and Immunity,
University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
* Author to whom correspondence should be addressed; E-Mail: [email protected];
Tel.: +44-(0)207-794-0500 (ext. 33109).
Received: 17 October 2013; in revised form: 11 November 2013 / Accepted: 13 November 2013 /
Published: 21 November 2013
Abstract: Primary infection with human cytomegalovirus (HCMV) results in the
establishment of a lifelong infection of the host which is aided by the ability of HCMV to
undergo a latent infection. One site of HCMV latency in vivo is in haematopoietic
progenitor cells, resident in the bone marrow, with genome carriage and reactivation being
restricted to the cells of the myeloid lineage. Until recently, HCMV latency has been
considered to be relatively quiescent with the virus being maintained essentially as a “silent
partner” until conditions are met that trigger reactivation. However, advances in techniques
to study global changes in gene expression have begun to show that HCMV latency is a
highly active process which involves expression of specific latency-associated viral gene
products which orchestrate major changes in the latently infected cell. These changes are
argued to help maintain latent infection and to modulate the cellular environment to the
benefit of latent virus. In this review, we will discuss these new findings and how they
impact not only on our understanding of the biology of HCMV latency but also how they
could provide tantalising glimpses into mechanisms that could become targets for the
clearance of latent HCMV.
Keywords: cytomegalovirus; latency; immune evasion; apoptosis; gene expression;
cellular signalling
OPEN ACCESS
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1. Introduction
Human Cytomegalovirus (HCMV) remains a major cause of disease in a number of patient
populations who have compromised immune systems, as well as providing an increasing threat to
critically ill immuno-competent patients [1–4]. These pathologies associated with opportunistic
HCMV infections can be, in part, associated with a key characteristic of the virus: the ability to
establish lifelong latent infection of the human host and, crucially, reactivate [2,5]. A wealth of studies
from a number of laboratories using naturally latently infected cells has led to an informed consensus
that the cells of the myeloid lineage represent at least one important site of HCMV latency,
persistence, and reactivation (reviewed in [6]). Thus, at a cellular level, there is a clear and intimate
link between myeloid differentiation and natural HCMV reactivation [7–14]. Furthermore, the use of
experimental infection of non-permissive primary cells and cell lines in vitro are generating snapshots
of the complex regulation of HCMV gene expression at a molecular level [15–25]. However, these
studies have focussed predominantly on the regulation of major immediate early (MIE) gene
expression because the critical switch to a reactivating phenotype is dependent on the triggering of
MIE gene expression from quiescence.
In many cases, the species specificity of HCMV has driven these analyses to be performed in
experimental cell culture models and, ultimately, on tissue derived from healthy HCMV seropositive
individuals which has then been analysed ex vivo. As a result, the mechanisms that control HCMV
latency and persistence in vivo, at an organism level, have relied on the extrapolation of studies
performed in vitro or using animal model surrogates such as murine CMV [26]; guinea pig CMV [27]
and, more recently, non-human primate CMV strains [28]. Consequently, the inability to perform
analogous studies in humans has likely contributed to the perception that HCMV latency is essentially
a relatively quiescent infection. However, as techniques for studying HCMV at a molecular level have
become increasingly powerful, it is now emerging that latent HCMV infection profoundly modulates
the latently infected cell and the surrounding cellular environment. These effects act in concert to
maintain latent carriage and this depends on, at least in part, the expression of a subset of virally
encoded gene products.
In this short review, we will examine our current knowledge of HCMV latency with particular
emphasis on recent data which suggest that HCMV imparts a distinctive signature on latently infected
cells. These latency-associated changes underpin the successful persistence of this virus in vivo and,
importantly, could direct novel therapeutic strategies to target latency and reactivation of this
important human pathogen.
2. Background—HCMV Latency and Reactivation
Following primary infection, HCMV establishes a latent infection of the CD34+ haematopoietic
cell population in the bone marrow [29,30]. The prevailing view is that, ultimately, the major
immediate early promoter (MIEP) is profoundly suppressed in these cells [6] and that this is achieved
through cellular transcriptional repressors directing histone-modifying enzymes to impart repressive
post-translational modifications of MIEP-associated histones [6]. During latency, the chromatin
structure of the MIEP bears all the hallmarks of transcriptional repression: tri-methylation of histone H3
(lysine 9 and 27) and recruitment of heterochromatin protein-1 (HP-1) coupled with a concomitant
Viruses 2013, 5 2805
absence of histone acetylation on histone H4 [11,16,17,25]. Consequently, HCMV MIE gene
expression, and lytic gene expression in general, is profoundly repressed in CD34+ progenitor cells.
This chromatin phenotype is maintained in the monocyte cells derived from these progenitors [11,31]
and it is only upon cellular differentiation that robust IE gene expression is observed [7,8,11,12,32].
The detection of IE gene expression in dendritic cells (DCs) is consistent with the histone
modifications present at the MIEP in these terminally differentiated myeloid cells [11,31]. For
instance, HP-1 is no longer associated with the MIEP—likely due to extensive de-methylation of histones
at lysine residue 9 (methylation at this residue being important for HP-1 binding to chromatin [33]) and, in
these cells, the MIEP is associated with predominantly acetylated histones. Thus, the presence of
repressive or activatory chromatin marks around the MIEP correlates with the expression of viral
major IE RNA and the latency/reactivation phenotype of the virus [11,31]. Importantly, and consistent
with molecular analyses, infectious HCMV progeny cannot be recovered from myeloid progenitor
cells i.e., CD34+ cells or granulocyte–macrophage progenitors (GMPs) unless they are co-cultured
under conditions that promote cellular differentiation or activation [9,11,34]. Analogous models of
histone-mediated regulation of viral lytic gene expression also underpin studies of herpes simplex
virus and Epstein–Barr virus and thus represent a common unifying theme in the biology of
herpesvirus latency and reactivation [35,36].
The molecular model of HCMV latency in the myeloid lineage, derived from analyses of natural
latency, has been reviewed extensively elsewhere [6,37,38] and has helped provide an initial
understanding of the underlying mechanism for the differentiation-dependent reactivation of HCMV. It
is worth noting, however, that other studies using experimental infection models of latency and
reactivation have essentially recapitulated the key observations made with natural models of latent
infection and this gives confidence that wider studies involving experimentally latent models will have
in vivo relevance.
2.1. The Transcriptional Landscape of Latent HCMV
HCMV encodes anywhere between 170 and 751 ORFs all of which are believed to be expressed at
some stage during lytic infection [39,40]. Furthermore, the virus also encodes a number of microRNAs
(miRNAs) which, during lytic infection, have been shown to target and regulate both cell and viral
gene expression [41–43]. In contrast, the transcriptional landscape in latency is less clear. The earliest
studies identified a number of transcripts arising from the MIE region of HCMV but no function was
assigned to them [44,45]. Furthermore, deletion of the putative ORFs encoded by these latency-associated
transcripts appeared to have little effect on HCMV latency in vitro [46]. As such, it was speculated that
HCMV could exist in latency in a relatively quiescent state and that the normal transit and
differentiation of latently infected CD34+ cells into the periphery was sufficient to trigger HCMV
reactivation. Indeed, transcriptional quiescence during latency would provide the ideal mechanism for
evasion of the robust immune responses known to be present in HCMV seropositive individuals [47].
However, a number of aspects of the known biology of HCMV are at odds with the view that HCMV
is maintained in a totally quiescent state. For instance, if virus is carried long-term in the myeloid
lineage, how is the latent genome maintained in cells which will, at least at some stage of their
lifespan, proliferate? Although no latent origin of replication has been definitively identified for
HCMV, it has been suggested that a mutation in the MIE region had a carriage defect during latency in
Viruses 2013, 5 2806
GMPs [48] and more recent work has suggested UL84 may act to maintain viral sequences [25].
Furthermore, an overt characteristic of HCMV latency is the carriage of the viral genome in the cells
of the myeloid lineage and, particularly, the monocyte lineage [49–51] but not lymphocyte or
polymorphonuclear cells [50] despite the fact that latent infection is seeded in a pluripotent progenitor
cell type [29,30]. Potentially, this could be explained in alternative ways: the virus actively promotes
myelopoiesis of infected CD34+ cells or, HCMV may preferentially promote the survival of myeloid
committed progenitors or, finally, HCMV cannot combat anti-viral mechanisms in cells committed to
the lymphoid lineage. Arguably, all these scenarios suggest an active process involving viral
latency-associated functions during latent infection.
A number of studies over the last 10 years or so have applied increasingly sensitive techniques to
determine whether viral gene expression occurs during latent infection. Two independent microarray
analyses identified a number of transcripts expressed during experimental latency [34,52] and,
importantly, some have been subsequently confirmed during natural latency; including UL138,
UL81-82ast (LUNA), as well as a splice variant of UL111A, which encodes a viral interleukin 10
(vIL-10) termed LAcmvIL-10 [24,53–55]. These, and subsequent studies, have also shown that the
initial infection of undifferentiated myeloid cells with HCMV to establish experimental latency results
in a burst of temporally dysregulated viral transcription from a number of gene loci, including MIE
gene expression, at very early times post infection [25,32,34]. However, it remains unclear what this
means in the context of latent infection. It is tempting to speculate that this gene expression is
important for preparing the cell for latency—akin to that proposed for the establishment of EBV
latency [56]. However, there is no evidence, as yet, that cells which initially express lytic antigens go
on to establish long-term latency. It is possible that the extremely high MOIs used to establish latent
infections in vitro results in a sub-population of lytically or abortively infected cells which are,
ultimately, unviable and die, leaving the true latent population.
Regardless, what is generally accepted is that HCMV has a very distinct transcriptional profile
during latent infection, quite different from lytic infection. The expression of a number of viral genes
has now been described during latency and these are summarised in Table 1. For the remainder of this
review, we will focus on emerging stories regarding the manipulation of latently infected cells by
HCMV and how, in some instances, viral gene products may contribute to this.
Table 1. Gene products and functions during latency and lytic infection.
Gene Product Latent Function Lytic Function References
CLTs Unknown Regulation of anti-viral 2’5’ OAS
expression (ORF94)
[44–46,57]
UL138 Regulation of TNFRI (up) and MRP1
(down), repression of the MIEP(?)
Regulation of TNFRI (up) and
MRP1 (down), virus maturation
(133-138 locus)
[53,58–61]
UL81-82ast Promotes UL138 gene expression. Unknown [24,55,62]
LAvIL-10 Down-regulation of MHC class II
expression, immune evasion
Unknown—cmvIL-10 expressed
during lytic infection
[54,63]
Lnc4.9 Binds Polycomb repressor complex 2,
Silencing of the MIEP
Unknown [25]
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Table 1. Cont.
Gene Product Latent Function Lytic Function References
UL84 Genome maintenance DNA replication, UTPase
activity, transcriptional
regulation
[25,64–67]
US28 Unknown GPCR, induces cell signalling and
cell migration, agonist of the MIEP
[68–74]
UL144 Unknown TNF superfamily member, hijacks
NF-kB signalling, immune
evasion?
[75–78]
3. Mechanisms Targeted during HCMV Latency
3.1. Viral Evasion of Cell Death
Pro-death signals in response to infection represent a very significant obstacle for many pathogens.
Consequently, key players in the cellular apoptotic response become important targets for the
virus—and HCMV is no exception. HCMV encodes an impressive armoury of anti-apoptotic functions
that it expresses throughout lytic infection and which all contribute to efficient virus infection [79–84].
However, there is no evidence that any of these already-described anti-apoptotic viral genes associated
with lytic infection are also expressed during latency. Clearly, if the virus was to be carried truly
silently during latency then, arguably, there would be little requirement for any increased protection
from cell death. However, it is becoming increasingly evident that HCMV does actively modulate
multiple functions of the latently infected cell and that these, in effect, stress the cell to the point that
viral functions are needed to protect the latently infected cell from such stress-induced pro-death signals.
In the context of infection, be it latent or lytic, the initiation of cell death can arise at the earliest
point of infection: at entry [85]. Pathogen recognition receptors (PRRs) can detect pathogen-associated
molecular patterns (PAMPs), triggering cell death—and this is an important part of an intrinsic
immune response [85]. Clearly, during lytic infection, the rapid expression of virally encoded
anti-apoptotic proteins could quickly provide protection against such extrinsic death response signals [80].
However, during HCMV infection of cells destined to become latently infected with the associated
suppression of the lytic transcription programme, it appears that virus binding, in itself, activates cell
survival signals [86,87]. This occurs in both CD34+ cells and CD14+ cells, albeit with the
employment of different signalling pathways in the two cell types as well as cell-specific differences in
the duration of the survival response. Nevertheless, the up-regulation of an important cellular
anti-apoptotic protein, MCL-1 [88], appeared to be important for protection in both cell types [86,87].
Thus, although the exact mechanisms of protection varied in these different cell types, the outcome
was the same.
The transitory nature of the ERK-MAPK dependent survival signal observed in CD34+ cells [86]
argues that is likely to be important for overcoming the initial death signals triggered by cellular
recognition of virus shortly after binding and/or entry. Consequently, it could be argued that long-term
anti-death signals may not be required by a virus which is truly silenced in latency. However, recent
work suggests that long-term anti-death signals may be important during latent infection with HCMV
Viruses 2013, 5 2808
(Figure 1). For instance, experimental latent infection of granulocyte–macrophage progenitors has
been shown to result in long-term up-regulation of PEA-15 RNA [89]. As PEA-15 is an anti-apoptotic
factor that blocks both TNFR1 and Fas-L triggered apoptosis [90], clearly its up-regulation could be
part of a protective response mediated by latent infection. Consistent with this, latently infected
CD34+ cells are protected from FAS-L induced cell death [91]. Furthermore, given that it has been
shown that the UL138 gene product up-regulates TNFR1 expression during lytic [59,60] and latent
infection [61], potentially sensitising latently infected cells to TNFR1 mediated apoptosis, the
concomitant up-regulation of PEA-15 would be a sensible pro-survival strategy. Other preliminary
data from the Sinclair laboratory has also shown that a number of other cellular proteins with potent
anti-apoptotic function are up-regulated in latently infected CD34+ cells (J.S. unpublished data) and
this includes the PEA-15 protein, further supporting a model by which induction of PEA-15 during
latent infection, at least in part, protects latently infected cells from pro-death signals. Furthermore, it
is likely that these effects are driven by secreted products in the latency-associated secretome [92],
since inhibition of latency-induced cellular IL-10 was sufficient to block this survival effect [91].
Figure 1. Protection of latently infected cells from cell death. CD34+ cells latently infected
with HCMV down-regulate the expression of mir92a. A key target of miRNA is the
GATA-2 transcription factor which, consequently, is up-regulated. This promotes
increased transcription of cellular (IL-10) and viral (LUNA) genes. LUNA expression
promotes UL138 gene expression—a gene product shown to up-regulate cell surface levels
of TNFRI, a potentially pro-apoptotic signalling factor. However, HCMV also up-regulates
a number of anti-apoptotic factors including PEA-15. This occurs, in part, via the
expression of IL-10 and potentially could provide a mechanism to protect cells from
extrinsic cell death signalling.
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3.2. Viral Evasion of the Immune Response during Latent Infection
HCMV infection is known to generate a robust T cell response in vivo with between 0.5 and 10% of
all cytotoxic T lympohcytes (CTLs) recognising HCMV antigens [47]. The CTL response to HCMV is
dominated by two abundant viral antigens—pp65 and IE72 [47], although CTLs which recognise
most, if not all, lytic antigens have been detected [93]. Pertinent to this review is that significant T cell
responses against antigens also expressed during latency are present in healthy HCMV carriers [94,95]
and thus, in theory, a latently infected cell should be visible to these T cells. However, recent work
suggests that latent infection results in a number of mechanisms which act in concert to disrupt these T
cell responses, thereby preventing clearance of latently infected cells by the adaptive arm of the host
immune response (Figure 2).
A recent analysis of experimentally latently infected CD34+ cells detected a unique cell secretome
signature associated with latency [92]. Intriguingly, this secretome was observed to promote the
migration of Th1 CD4+ T cells to the latently infected cell. However, the anti-viral effector functions
of these recruited cytotoxic T cells was countered by the concomitant latency-associated expression of
two key cellular cytokines, transforming growth factor—beta (TGF-) and interleukin-10 (cIL-10).
Both TGF- and cIL-10 have profound immune-modulatory capacity [96] and, consistent with this,
blocked the CD4+ T effector functions [92]. Although the exact mechanisms that resulted in
up-regulated expression of TGF- and cIL-10 during latency are unclear, elevated cIL-10 production
was observed to be, at least partly, dependent on the up-regulation of the cellular GATA-2
transcription factor resulting from a concomitant down-regulation of the cellular microRNA mir92a [91].
Furthermore, other recent work has illustrated that a proportion of the CD4+ T cell response directed
against latent antigens consists of T regulatory (Treg) cells [95]. This study in healthy donors showed
that, whilst cytotoxic CD4+ T cell responses against latent antigens were detectable, they were
dominated by IL-10 expressing Treg cells. Consequently, the recruitment of Treg cells to a latently
infected cell (74) would augment the effects of the immune-suppressive secretome around the latently
infected cells dampening down CTL effector cell function [92]. Given the extremely low frequency of
latently infected cells in a healthy seropositive individual [97], it is likely that the microenvironment
around a latently infected cell would have little overall impact on the normal immune homeostasis of
the bone marrow but may be locally sufficient to ensure latently infected cells evade elimination by the
immune system.
Induction of cIL-10 by latent virus clearly appears to be of real import for latent carriage and this
view is, perhaps, reinforced by the fact that HCMV also encodes an IL-10 homolog, known as cmvIL-10,
which is expressed solely during lytic infection, as well as an alternatively spliced form (LAcmvIL-10)
expressed during both latent infection and lytic infection [98,99]. Interestingly, lytic infection-
associated cmvIL-10 has retained many of the immune-suppressive functions associated with its
cellular counterpart [100–102] and, indeed, signals via the human IL-10 receptor [98,103]. Consistent
with a role for cmvIL-10-mediated immune evasion are studies in rhesus CMV that have demonstrated
a role in viral dissemination [104]—presumably via a temporary dampening of the immune response.
It is tempting to speculate that failure to evade the immune response during a primary infection could
profoundly impact on the set point of latency but, unfortunately, this has not been possible to analyse.
Viruses 2013, 5 2810
Figure 2. Evasion of the immune response to HCMV. The up-regulation of IL-10 in
latently infected CD34+ cells is concomitant with TGF-b up-regulation via an unknown
mechanism. However, the expression of two potent immune-suppressive cytokines inhibits
the effector functions of CD4 Th1 cells recruited to a latently infected cell. Furthermore,
both cellular IL-10 and viral IL-10 (LAcmvIL-10) act in concert to promote the
down-regulation of HLA-DR MHC class II molecules on the surface of latently infected
cells. Although the mechanism used by LAcmvIl-10 is not yet understood but is known not
to occur via binding to the cellular IL-10 receptor.
As stated above, the cmvIL-10 gene encodes a number of biological properties that could impinge
on HCMV latency and reactivation. Multiple studies have shown that cmvIL-10 promotes MHC class I
and II down-regulation [102], prevents DC maturation and function [105,106] and promotes the
polarisation of macrophages to an M2c phenotype [107]—which is considered to be a relatively
inactive macrophage phenotype compared with the classic inflammatory M1 phenotype. As such, all
these functions would be consistent with a role in immune evasion. However, the alternatively spliced
LAcmvIL-10, though also detected during lytic infection, is the isoform expressed during latent
infection [54] but does not exhibit many of the properties of cmvIL-10 [63]—presumably, in part, due
to its inability to bind the cIL-10 receptor [63]. Crucially, however, both latently infected GMPs and
monocytes have been shown to exhibit a dramatic decrease in cell surface expression of MHC
class II [32,108]—a function associated with LAcmvIL-10 [63]. Importantly the deletion of the
UL111A locus from the virus (and thus LAcmvIL-10) has illustrated that latently cells become
sensitive to CD4+ recognition and killing [109] as well as impacting on the normal differentiation of
Viruses 2013, 5 2811
myeloid progenitor cells to a DC phenotype [110]. Thus despite a loss of many of the functions
associated with cmvIL-10, the LAcmvIL-10 isoform has retained biological properties that could
contribute to successful persistence during latency in vivo.
3.3. Viral Regulation of Immediate Early Gene Expression
As already discussed, the regulation of HCMV MIE gene expression during latency involves the
action of higher order chromatin structure. As such, it has been hypothesised that the assembly and
modification of histones at the MIEP is an intrinsic response dictated by the cellular environment.
Indeed, at low MOIs during lytic infection, there appears to be pre-immediate early gene expression
event where the MIEP is associated with methylated histones [111]. This may well represent an
anti-viral response to foreign DNA that is mediated by ND10 bodies and their components and is
overcome by the action of incoming viral pp71 tegument protein and, subsequently, newly expressed
IE72 which has been reviewed extensively elsewhere [112–114]. In contrast to lytic infection, the
intrinsic repression of the MIEP is not overcome in non-productive myeloid cells. One study has
proposed that unknown mechanisms that exclude pp71 from the nucleus in CD34+ cells contributes to
this [23], although the high levels of transcriptional repressors present in these cells is also likely to be
important; consistent with this, the transfected MIEP is intrinsically less active in undifferentiated myeloid
cells [115]. Indeed, a number of transcriptional repressors of the MIEP have been identified (such as
YY1 and ERF) and these are believed to recruit histone methyltransferases [116,117] to the MIEP in
undifferentiated myeloid cells and this is important for generating the signature repressive chromatin
phenotype associated with the MIEP of latent HCMV [11].
However, more recent work suggests that HCMV gene products themselves may be actively
helping to manage MIE regulation during HCMV latency. Although the prevailing view of the MIEP
during latency in CD34+ cells is a promoter predominantly associated with repressive chromatin
marks (i.e., histone methylation and HP-1 binding), chromatin and its post-translational modification is
highly dynamic. Studies analysing the chromatin state of well-characterised silenced cellular genes, in
e.g., stem cells, suggest that all cellular promoters bear at least some hallmarks of transcription [118].
Histone methylation at lysine 4 (a marker of a recently transcribed promoter) has been identified at
“silent promoters” and, consistent with this, small RNA fragments were identified which would
correspond to aborted transcription events [118]. Thus the notion of “chromatin breathing,” even at
repressed promoters, is not uncommon. Given the potent activity of the MIEP, there is a strong
argument that the MIEP is unlikely to be completely transcriptionally repressed, even in the most
undifferentiated myeloid cell, and that this will call for additional mechanisms to eliminate any
residual low level, uncontrolled MIE expression (Figure 3).
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Figure 3. HCMV mediated repression of IE gene expression. Latent infection of CD34+
cells is characterised by a repression of the major immediate early promoter (MIEP).
Classically, the MIEP has been shown to be repressed by multiple cellular transcriptional
repressors known to interact with components of the histone modifying enzyme families.
However, these events may be augmented by the activity of further viral mechanisms. The
expression of LUNA during latency has been shown to be important for UL138
expression—a protein postulated to repress the MIEP. Furthermore, the expression of the
long non-coding 4.9kb RNA (lnc4.9 RNA) during latency has been suggested to promote
the recruitment of polycomb repressor complex 2 (PRC2) to the MIEP via direct binding of
the RNA. Recruitment of PRC2 would promote a chromatin structure inhibitory for MIE
transcription. Finally, the expression of a viral miRNA, mir112.1, has been hypothesised to
be important for silencing translation from MIE transcript UL123 during latency.
During lytic infection, HCMV expresses a virally encoded microRNA (mirUL-112-1) that
specifically target IE72 encoding UL123 transcripts [119,120] and inhibits IE72 translation [120].
Deletion of mirUL-112-1 has no overt phenotype in infected fibroblasts, likely due to the substantial
levels of IE72 transcript accompanying lytic infection [120]. However, it has been postulated that low
levels of IE72 RNA may be targeted efficiently and, hence, miRUL112-1 may have more of a role
during latency [119]—where untimely IE72 expression could be problematic but where the less
abundant levels of IE72 RNA could be more effectively controlled by a miRNA-mediated
mechanisms. In effect, the microRNA acts as a safety net to ensure that the functional impact of any
sporadic activity of the MIEP, and any resultant IE transcripts, are minimised during latent infection.
A more recent study [25] that used a deep sequencing approach to re-visit latent gene expression in
experimental as well as naturally latent tissue samples, identified the expression of a number of viral
Viruses 2013, 5 2813
transcripts including a 4.9 kb long non-coding RNA (lnc4.9). Interestingly, this transcript was
observed to associate with the polycomb repressor complex 2 (PRC2)—with direct analogy to the
KSHV PAN RNA species that also bind this complex [121]. Indeed, the PRC2 complex has also been
shown to regulate HSV latency, although this is thought to occur independently of direct binding to the
LAT RNA [122]. Furthermore, the binding of components of PRC2 and also the lnc4.9 RNA was
observed in experimentally latently infected cells [25]. The net result of such interactions would be to
augment the silencing of the viral MIEP linked with histone tri-methylation at lysine 27 on histone H3.
The overall contribution of the lnc4.9 RNA to HCMV latency remains to be determined; however,
analysis of whether virus mutants that fail to express lnc4.9 are defective in their establishment and
maintenance of latency could help determine whether this interaction is as an essential component of
the mechanisms required to maintain HCMV latency.
Finally, other recent work has also suggested that the MIEP may repressed by a virally encoded
factor during latency [23]. Treatment with histone deacetylase inhibitors (HDACi) is insufficient to
promote the reactivation of IE gene expression in CD34+ cells latently infected with clinical strains of
HCMV [23]. Conversely, however, CD34+ cells latently infected with laboratory isolates are
responsive to HDACi. Consequently, this has suggested that a viral factor present in clinical isolates is
involved in chromatin-mediated suppression of MIEP activity during experimental latency [23]. The
likely candidate is UL138, which is expressed only in clinical isolates [39] and is known to be
expressed during latent infection [34,53]. However, published studies suggest that the importance of
UL138 for latency is not due to any direct effect on MIEP activity as a transcriptional repressor [58],
thereby remaining in line with the predominant localisation of UL138 protein to the Golgi apparatus
during lytic infection and transfection [58]. One caveat to this, though, is that the localisation of the
UL138 protein has not been extensively analysed during latent infection and hence, at this stage, a role
for UL138 in the repression of the viral MIEP during latency awaits further analyses.
3.4. Viral Regulation of Latent Gene Expression
In addition to the regulation of MIE gene expression, there is emerging evidence that HCMV also
expresses functions to ensure efficient latent gene expression during latent infection (Figure 3). This,
in itself, argues that latent viral gene products are likely to have important functions during latency
and, importantly, that these could act as potential therapeutic targets for latent infection.
The modulation of the cellular miRNAome during latent infection could provide potent fine-tuning
mechanisms to optimise both viral and cellular gene expression [91]. As discussed earlier, the
down-regulation of cellular hsa-miR-92a by HCMV is important for the increased cIL-10 production
that results in downstream effects on viability and immune modulation [91,92]. However, the
down-regulation of hsa-miR-92a also results in an increase in the levels of the GATA-2 transcription
factor [91]. The GATA family of proteins are considered key regulators of haematopoiesis and
myeloid cell production [123,124] and, thus, the targeting of this transcription factor in the knowledge
that HCMV persists in the myeloid lineage appears more than coincidental. However, a more direct
effect of GATA-2 regulation is observed on latent gene expression. A number of promoters of latently
expressed genes contain consensus sequences for GATA-2 binding sites [77,91,125,126] and two of
these, LUNA and UL144, have been directly demonstrated to be GATA-2 responsive [77,126]. Recent
work has shown that the down-regulation of the hsa-mir92a observed in HCMV infected CD34+ cells
Viruses 2013, 5 2814
results in increased GATA-2 levels during latency, subsequently leading to increased levels of
GATA-2-dependent latent gene expression [91].
Although we are far from completely elucidating the function of viral gene products during latency,
observations, to date, strongly argue that latent infection with HCMV results in a latency-associated
transcription profile of viral gene expression, resulting in an orchestrated change in the cell to support
latent carriage. The regulation of latent viral gene expression, as well as the role of latent viral
functions and their effects on cellular gene expression, are clearly inextricably linked. For instance,
recent work from the St Jeor laboratory has shown that the expression of LUNA during latent infection
is also important for latency-associated UL138 gene expression [62]. Consequently, a pathway of
interactions appears to occur during latency which is exemplified by latency, thus resulting in the
targeting of cellular hsa-miR92a; this, in turn, up-regulates cellular GATA-2 expression [91], leading
to a downstream impact on latency-associated LUNA gene expression [77,91] and ultimately ensuring
the expression of UL138 [62], which has been proposed to be a key determinant of latency [23,53].
Clearly, this simplified example of a linear pathway of viral and cellular interactions is likely to
give way to far more complex networks of host–virus interactions as we begin to understand the
multi-functional role of viral proteins, non-coding RNAs, and miRNAs during HCMV latency and
their impact on the latent cell.
4. Concluding Remarks
The advances in molecular techniques for performing large-scale analyses at the cell level are
allowing ever more detailed analyses of aspects of HCMV biology which, previously, were all but
impossible due the limitations of sensitivity and the availability of tractable primary cell models. These
approaches have already begun to illustrate the complexity of HCMV latency and to provide an
intriguing view of the concerted efforts HCMV employs to maintain the latent state.
It is evident that the reductionist approach of these types of studies, as well as the difficulty in
further examining in vitro findings in vivo, warrants necessary caution to prevent overinterpretation.
Accordingly, a key development in the future of HCMV studies of latency and reactivation will be the
tractability and applicability of the humanised mouse model to studies of HCMV [127]. Caveats with
this system also remain; although the humanised mouse can be used to assess HCMV reactivation in
the myeloid lineage in vivo, this is still occurring in the background of mouse tissue that does not
support extensive HCMV replication [128]. Consequently, such analyses are, arguably, restricted to
the very initial events of HCMV reactivation occurring within a specific niche of human cells.
Furthermore, the extent to which the human haematopoietic system develops from engrafted human
CD34+ cells in the mouse (for instance, murine and human cytokines do not crosstalk unequivocally)
is unclear and, more generally, the extent to which mouse models of disease truly reflect the human
condition is an area of ongoing debate [129,130]. Nevertheless, the humanised mouse model could
provide the potential to examine a number of predictions regarding HCMV latency derived from in
vitro studies, as well as certain aspects of the development of the immune response to latent HCMV.
These cautionary notes aside, the identification of viral gene functions expressed during
experimental latency (many of which, importantly, can be validated in naturally latent cells ex vivo) is
beginning to provide a tantalising glimpse into the once-perceived “black box” of latency. As we begin
to understand the functions of these latency-associated gene products, and assess their precise role in
Viruses 2013, 5 2815
HCMV latency and reactivation, they are also likely to become potential targets for therapeutics. These
approaches could range from the targeting of factors important for HCMV reactivation (our own
unpublished work suggests that the LUNA gene product may encode a function that could be a future
therapeutic target) or for the direct targeting of latently infected cells using chemotherapeutic or
immunotherapeutic means [61].
Anti-viral strategies for HCMV have, to date, relied on targeting of replicating virus during lytic
infection. However, understanding the complex interplay between the virus and the host during latency
will give important insights into how to explore potential therapeutic options that target latent virus in
what was previously considered to be in an “untargetable state.”
Acknowledgments
We would like to thank members past and present of the Sinclair laboratory and the numerous
colleagues in the field whose work has contributed to this review. We also apologise to those
colleagues whose work has not been cited due to space limitations. Finally, we gratefully acknowledge
funding from the UK Medical Research Council (J.H.S. G:0701279 and M.B.R. G:0900466) which
supports the current research in our laboratories and also the support of NIHR UK Biomedical
Research Centre (J.H.S.).
Conflicts of Interest
The authors declare no conflict of interest.
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